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The identification and quantification of phosphorylated amino acids, peptides and proteins is one of the key challenges in contemporary bioanalytical research, noteworthy to diagnose and treat diseases at an early stage. Small sensing devices like microfluidic chips combined with “smart” detection chemistry and simple data assessment, processing and presentation are attractive in this regard. We developed novel synthetic probes, targeting phosphorylated amino acids, based on core-shell microparticles consisting of a silica core coated with a molecularly imprinted polymer shell (MIP). These “plastic antibodies” which are extremely robust, resist denaturing solvents and high temperatures, can be reproducibly produced at low cost, can potentially overcome many of the problems in the current detection strategies. The MIP layer, containing a fluorescent probe monomer, responds to phosphorylated amino acids such as phosphorylated tyrosine (pTyr) with a significant imprinting factor, i.e. selectivity, higher than 3.5, and a “lighting-up” of its fluorescence accompanied by the development of a strongly red-shifted emission band. The bead-based ratiometric detection scheme has also been successfully transferred to a microfluidic chip format to demonstrate its applicability to rapid assays. Such a device could yield an automated pTyr measurement system in the future. The setup was built by coupling a PDMS/Teflon/glass microfluidic chip with an optical setup for fluorescence measurements able to extract and monitor pTyr concentration from 0.5–200 μM.